Chapter 2: The Chemistry of Life – Foundations for Anatomy & Physiology

2.1 Atoms and Elements

Atoms: Structure and Properties

An atom is the smallest unit of matter that retains the properties of an element. Atoms are composed of three main subatomic particles:

• Protons: Positively charged particles found in the nucleus.

• Neutrons: Neutral particles also located in the nucleus.

• Electrons: Negatively charged particles that orbit the nucleus in electron shells.

Each electron shell can hold a specific maximum number of electrons:

• First shell: 2 electrons

• Second shell: 8 electrons

• Third shell: up to 18 electrons, but is stable with 8 (the octet rule)

The valence shell is the outermost electron shell and determines an atom's chemical reactivity.

Elements and the Periodic Table

• An element is a substance composed of one or more identical atoms, defined by their number of protons (atomic number).

• The four major elements in the human body are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N).

• The periodic table organizes elements by increasing atomic number and groups them by similar chemical properties (metals, non-metals, metalloids).

Chemical Notation

• Atomic Symbol: 1 or 2 letter abbreviation for each element (e.g., C for carbon).

• Atomic Number: Number of protons in the nucleus.

• Mass Number: Total number of protons and neutrons.

• Atomic Weight: Average mass of all isotopes of an element, weighted by their natural abundance.

Isotopes and Atomic Weight

• Isotopes are atoms of the same element with different numbers of neutrons (e.g., Carbon-12, Carbon-13, Carbon-14).

• Radioisotopes are unstable isotopes that undergo radioactive decay, releasing energy and particles. They are used in nuclear medicine and radiation therapy.

2.2 Combining Matter: Mixtures & Chemical Bonds

Mixtures

Mixtures are physical combinations of two or more substances where each retains its original properties. They can be separated physically and do not involve chemical bonding.

• Suspensions: Large particles that settle out (e.g., blood cells in plasma).

• Colloids: Intermediate particles that do not settle (e.g., cytosol in cells).

• Solutions: Small particles dissolved in a solvent (e.g., glucose in water).

Solutions, Solvents, and Solutes

• Solute: Substance that is dissolved.

• Solvent: Substance in which the solute dissolves (water is the universal solvent in biology).

• Solubility: Degree to which a solute dissolves in a solvent.

• Concentration: Amount of solute in a solution, often expressed as a percentage.

Chemical Bonds

• Molecules: Two or more atoms chemically bonded together (e.g., O2).

• Compounds: Molecules composed of atoms from different elements (e.g., H2O).

• Molecular formulas show the types and numbers of atoms (e.g., C6H12O6).

Valence Electrons and the Octet Rule

• Chemical bonds form when valence electrons interact.

• The octet rule: Atoms are most stable with 8 electrons in their valence shell.

• Atoms with filled valence shells are inert; those without will react to achieve stability.

Types of Chemical Bonds

• Ionic Bonds: Formed by the transfer of electrons from a metal to a non-metal, resulting in charged ions (cations are positive, anions are negative).

• Covalent Bonds: Formed by the sharing of valence electrons between non-metals. Can be single, double, or triple bonds depending on the number of shared electron pairs.

Polar vs. Non-Polar Bonds

• Nonpolar covalent bonds: Electrons are shared equally (e.g., H2).

• Polar covalent bonds: Electrons are shared unequally, creating partial charges (e.g., H2O).

• Electronegativity: The ability of an atom to attract electrons; increases across a period and up a group in the periodic table.

Hydrogen Bonds

• Weak attractions between polar molecules (e.g., between water molecules).

• Responsible for properties like surface tension and the structure of proteins and DNA.

2.3 Energy & Chemical Reactions

Energy in Biological Systems

• Energy: The capacity to do work.

• Potential energy: Stored energy due to position.

• Kinetic energy: Energy of motion.

• Energy can be chemical, electrical, or mechanical in biological systems.

• Law of Conservation of Energy: Energy cannot be created or destroyed, only converted.

Chemical Reactions

• Anabolic (synthesis) reactions: Build larger molecules from smaller ones (A + B → AB).

• Catabolic (decomposition) reactions: Break down molecules into smaller units (AB → A + B).

• Exchange reactions: Atoms are exchanged between molecules (AB + CD → AD + BC).

• Redox (oxidation-reduction) reactions: Involve the transfer of electrons. Oxidation is loss of electrons, reduction is gain of electrons.

Endergonic and Exergonic Reactions

• Endergonic reactions: Require energy input; products have more energy than reactants.

• Exergonic reactions: Release energy; products have less energy than reactants.

Reversible Reactions

• Can proceed in both forward and reverse directions.

• Example: $\mathrm{H_2CO_3 \rightleftharpoons H^+ + HCO_3^-}$ (carbonic acid dissociating into hydrogen and bicarbonate ions)

Reaction Rates and Activation Energy

• All chemical reactions require activation energy to get started.

• Factors affecting reaction rate: concentration, temperature, properties of reactants, and presence of a catalyst.

Enzymes

• Enzymes are biological catalysts that lower activation energy and increase reaction rates.

• Highly specific for substrates and reactions.

• Not consumed or altered during the reaction.

• Examples: Alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH2), acetylcholinesterase.

2.4 Inorganic Compounds: Water, Acids, Bases, and Salts

Organic vs. Inorganic Compounds

• Organic compounds: Contain carbon bonded to hydrogen (e.g., carbohydrates, proteins, lipids, nucleic acids).

• Inorganic compounds: Generally do not contain carbon-hydrogen bonds (e.g., water, acids, bases, salts).

Properties of Water

• Makes up 50–65% of human body mass.

• Functions: transport, lubrication, cushioning, excretion of wastes, regulation of body temperature.

• High heat capacity and heat of vaporization, important for temperature regulation.

• Surface tension and adhesion due to hydrogen bonding.

Solubility in Water

• Hydrophilic: Water-loving; dissolves easily (e.g., ions, polar molecules).

• Hydrophobic: Water-fearing; does not dissolve (e.g., non-polar molecules).

• Amphipathic: Molecules with both hydrophilic and hydrophobic regions (e.g., phospholipids).

Acids, Bases, and pH

• Acids: Proton donors; increase H+ concentration in solution.

• Bases: Proton acceptors; decrease H+ concentration.

• pH scale: Measures H+ concentration; ranges from 0 (acidic) to 14 (basic), with 7 as neutral.

• Each pH unit represents a tenfold change in H+ concentration.

• Normal blood pH: 7.35–7.45.

• Buffers: Resist changes in pH; important for homeostasis (e.g., carbonic acid-bicarbonate buffer system).

Salts and Electrolytes

• Salts: Ionic compounds that dissociate in water to form electrolytes (charged particles).

• Electrolytes are essential for nerve impulse transmission, muscle contraction, and fluid balance.

2.5 Organic Compounds: Macromolecules

Carbohydrates

• Monomers: Monosaccharides (e.g., glucose, fructose, galactose).

• Disaccharides: Two monosaccharides joined (e.g., sucrose, lactose).

• Polysaccharides: Long chains (e.g., glycogen, starch).

• Function: Primary energy source for cells.

Lipids

• Types: Triglycerides (fats), phospholipids, steroids (e.g., cholesterol).

• Functions: Energy storage, cell membrane structure, hormone synthesis.

Proteins

• Monomers: Amino acids.

• Structure: Primary, secondary, tertiary, and quaternary levels.

• Functions: Enzymes, structural support, transport, signaling.

Nucleic Acids

• Monomers: Nucleotides (composed of a sugar, phosphate, and nitrogenous base).

• Types: DNA (deoxyribonucleic acid), RNA (ribonucleic acid).

• Function: Store and transmit genetic information.

ATP (Adenosine Triphosphate)

• Structure: Adenine base, ribose sugar, three phosphate groups.

• Function: Main energy currency of the cell; energy is released when phosphate bonds are broken.

Polymerization and Hydrolysis

• Dehydration synthesis: Bonds monomers together by removing water.

• Hydrolysis: Breaks bonds by adding water.

Summary Table: Key Terms and Definitions

Term	Definition
Atom	Smallest unit of an element retaining its properties
Element	Substance made of one type of atom
Isotope	Atoms of the same element with different numbers of neutrons
Ion	Charged atom (cation: positive, anion: negative)
Molecule	Two or more atoms bonded together
Compound	Molecule with atoms from different elements
Solute	Substance dissolved in a solvent
Solvent	Substance that dissolves the solute
pH	Measure of hydrogen ion concentration
Buffer	Substance that resists changes in pH
Enzyme	Biological catalyst that speeds up reactions

Additional info: This summary integrates and expands upon the provided slides and notes, ensuring all key concepts from Chapter 2 are covered for Anatomy & Physiology students.